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fix references to software in configuration file
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,24 +1,22 @@ | ||
| ### CONFIGURATION FILE FOR GWASTOOLKIT ### | ||
| # Precede your comments with a #-sign. | ||
| # | ||
| # Set the directory variables, the order doesn't matter. | ||
| # Don't end the directory variables with '/' (forward-slash)! | ||
| ### Precede your comments with a #-sign. | ||
| ### | ||
| ### Set the directory variables, the order doesn't matter. | ||
| ### Don't end the directory variables with '/' (forward-slash)! | ||
|
|
||
| # REQUIRED: Path_to where the software resides on the server. | ||
| SOFTWARE="/hpc/local/CentOS7/dhl_ec/software" | ||
| ### REQUIRED: Path_to where the software resides on the server. | ||
| SOFTWARE="/hpc/local/Rocky8/dhl_ec/software" | ||
|
|
||
| # REQUIRED: Path_to where GWASToolKit resides on the server. | ||
| ### REQUIRED: Path_to where GWASToolKit resides on the server. | ||
| GWASTOOLKITDIR="${SOFTWARE}/GWASToolKit" | ||
|
|
||
| # REQUIRED: Path_to support programs on the server | ||
| # SNPTEST="${SOFTWARE}/snptest_v2.5.2_CentOS6.5_x86_64_static/snptest_v2.5.2" | ||
| # SNPTEST="${SOFTWARE}/snptest_v2.5.4-beta3_linux_x86_64_static/snptest_v2.5.4-beta3" | ||
| SNPTEST="${SOFTWARE}/snptest_v2.5.6_CentOS_Linux7.8-x86_64_dynamic/snptest_v2.5.6" | ||
| PLINK2="${SOFTWARE}/plink_v1.9" | ||
| LOCUSZOOM13="/hpc/local/CentOS7/dhl_ec/software/locuszoom_1.3/bin/locuszoom" | ||
| ### REQUIRED: Path_to support programs on the server | ||
| SNPTEST="${SOFTWARE}/snptest_v2.5.6_CentOS_Linux7.8.2003-x86_64_dynamic/snptest_v2.5.6" | ||
| PLINK2="${SOFTWARE}/plink_v1.90_beta7_20230116" | ||
| LOCUSZOOM13="${SOFTWARE}/locuszoom_1.3/bin/locuszoom" | ||
|
|
||
| # REQUIRED: SLURM settings -- these should work universally | ||
| # FOR GWAS | ||
| ### REQUIRED: SLURM settings -- these should work universally | ||
| ### FOR GWAS | ||
| QMEMGWAS="8G" # '8Gb' for GWAS | ||
| QTIMEGWAS="12:00:00" # 12 hours for GWAS | ||
| QMEMGWASCLUMP="164G" # 16Gb needed for clumping | ||
|
|
@@ -36,19 +34,19 @@ QTIMEVAR="00:15:00" # 15mins for variants | |
| QMEMVARCLEANER="4G" # 4Gb needed for cleaner | ||
| QTIMEVARCLEANER="01:00:00" # 1hours to clean | ||
|
|
||
| # FOR VARIANT | ||
| ### FOR VARIANT | ||
| QMEMVAR="8G" # 8Gb for variants | ||
| QTIMEVAR="00:15:00" # 15mins for variants | ||
| QMEMVARCLEANER="4G" # 4Gb needed for cleaner | ||
| QTIMEVARCLEANER="01:00:00" # 1hours to clean | ||
|
|
||
| # FOR REGION | ||
| ### FOR REGION | ||
| QMEMREG="8G" # 8Gb for regions | ||
| QTIMEREG="00:30:00" # 30mins for regions | ||
| QMEMREGCLEANER="4G" # 4Gb needed for cleaner | ||
| QTIMEREGCLEANER="01:00:00" # 1hours to clean | ||
|
|
||
| # FOR GENE | ||
| ### FOR GENE | ||
| QMEMGENE="8G" # 8Gb for genes | ||
| QTIMEGENE="00:30:00" # 30 minutes for genes | ||
| QMEMGENEQC="4G" # 4 Gb for snptest qc | ||
|
|
@@ -58,53 +56,52 @@ QTIMEGENELZOOM="00:15:00" #15mins for locuszoom | |
| QMEMGENECLEANER="4G" # 4Gb needed for cleaner | ||
| QTIMEGENECLEANER="01:00:00" # 1hours to clean | ||
|
|
||
| # REQUIRED: mailing settings | ||
| # you're e-mail address; you'll get an email when the job has ended or when it was aborted | ||
| # 'BEGIN' Mail is sent at the beginning of the job; | ||
| # 'END' Mail is sent at the end of the job; | ||
| # 'FAIL' Mail is sent when the job fails. | ||
| # 'REQUEUE' Mail is sent when the job is re-queued; | ||
| # 'ALL' Mail sent for all the above. | ||
| ### REQUIRED: mailing settings | ||
| ### Your e-mail address; you'll get an email when the job has ended or when it was aborted | ||
| ### 'BEGIN' Mail is sent at the beginning of the job; | ||
| ### 'END' Mail is sent at the end of the job; | ||
| ### 'FAIL' Mail is sent when the job fails. | ||
| ### 'REQUEUE' Mail is sent when the job is re-queued; | ||
| ### 'ALL' Mail sent for all the above. | ||
| YOUREMAIL="[email protected]" | ||
| MAILSETTINGS="FAIL" | ||
|
|
||
|
|
||
| # ANALYSIS SETTINGS | ||
| # REQUIRED: Path_to where the main analysis directory resides. Make sure that it exists | ||
| ### ANALYSIS SETTINGS | ||
| ### REQUIRED: Path_to where the main analysis directory resides. Make sure that it exists | ||
| PROJECTDIR="/hpc/dhl_ec/svanderlaan/projects/SOMEDIR" | ||
|
|
||
| # REQUIRED: Name of the project, this will automatically be made. | ||
| ### REQUIRED: Name of the project, this will automatically be made. | ||
| PROJECTNAME="SOME_FANCY_PROJECTNAME" | ||
|
|
||
| # REQUIRED: Analysis settings. | ||
| # You can choose one of these options [GWAS/VARIANT/REGION/GENES]. | ||
| ### REQUIRED: Analysis settings. | ||
| ### You can choose one of these options [GWAS/VARIANT/REGION/GENES]. | ||
| ANALYSIS_TYPE="VARIANT" | ||
| # You can choose one of these options [AEGS/AAAGS/CTMM/UCORBIO/MYOMARKER/HELPFULL/RIVM]. | ||
| ### You can choose one of these options [AEGS/AAAGS/CTMM/UCORBIO/MYOMARKER/HELPFULL/RIVM]. | ||
| STUDY_TYPE="AEGS" | ||
|
|
||
| # REQUIRED | ||
| # Indicate the file extension used for the genetic data [bgen, gen, gen.gz, vcf, vcf.gz] | ||
| ### REQUIRED | ||
| ### Indicate the file extension used for the genetic data [bgen, gen, gen.gz, vcf, vcf.gz] | ||
| GENETICEXTENSION="vcf.gz" | ||
|
|
||
| # REQUIRED: give a list of covariates in a file | ||
| # Example covariate-list format: | ||
| # COHORT Age sex PC1_2013 PC2_2013 PC3_2013 PC4_2013 PC5_2013 PC6_2013 PC7_2013 PC8_2013 PC9_2013 PC10_2013 | ||
| ### REQUIRED: give a list of covariates in a file | ||
| ### Example covariate-list format: | ||
| ### COHORT Age sex PC1 PC2 | ||
| COVARIATE_FILE="${PROJECTDIR}/covariates.txt" | ||
|
|
||
| # REQUIRED: give a list of phenotypes to be analyzed | ||
| ### REQUIRED: give a list of phenotypes to be analyzed | ||
| PHENOTYPE_FILE="${PROJECTDIR}/phenotypes.txt" | ||
|
|
||
| # SPECIFIC DATA SETTINGS | ||
| # | ||
| # REQUIRED: location of [imputed] data to use -- all BGEN-format. | ||
| ### SPECIFIC DATA SETTINGS | ||
| ### REQUIRED: location of [imputed] data to use -- all BGEN-format. | ||
| # | ||
| # ### AEGS, 1000G phase 3, GoNL5 - bgen files | ||
| ### AEGS, 1000G phase 3, GoNL5 - bgen files | ||
| # IMPUTEDDATA="/hpc/dhl_ec/data/_ae_originals/AEGS_COMBINED_IMPUTE2_1000Gp3_GoNL5/aegs_combo_1kGp3GoNL5_RAW_chr" | ||
| # ### AEGS, 1000G phase 1 | ||
| ### AEGS, 1000G phase 1 | ||
| # IMPUTEDDATA="/hpc/dhl_ec/data/_ae_originals/AEGS_COMBINED_IMPUTE2_BBMRI_1000Gp1v3/aegs_combo_1000g_RAW_chr" | ||
| # ### AEGS, GoNL4 | ||
| ### AEGS, GoNL4 | ||
| # IMPUTEDDATA="/hpc/dhl_ec/data/_ae_originals/AEGS_COMBINED_IMPUTE2_BBMRI_GoNL4/aegs_combo_gonl4_RAW_chr" | ||
| # ### AEGS, 1000G phase 3 and HRC r1.1 combined (Michigan Imputation Server) - vcf.gz files | ||
| ### AEGS, 1000G phase 3 and HRC r1.1 combined (Michigan Imputation Server) - vcf.gz files | ||
| IMPUTEDDATA="/hpc/dhl_ec/data/_ae_originals/AEGS_COMBINED_EAGLE2_1000Gp3v5HRCr11/aegs.qc.1kgp3hrcr11.chr" | ||
| IMPUTEDDATA_CHRX="/hpc/dhl_ec/data/_ae_originals/AEGS_COMBINED_EAGLE2_1000Gp3v5HRCr11/_chr23_1kg_gonl5/aegs.1kgp3gonl5.chr" | ||
|
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||
|
|
@@ -115,23 +112,23 @@ IMPUTEDDATA_CHRX="/hpc/dhl_ec/data/_ae_originals/AEGS_COMBINED_EAGLE2_1000Gp3v5H | |
| ### AAAGS, HRC r1.1 (Michigan Imputation Server) | ||
| # IMPUTEDDATA="/hpc/dhl_ec/data/_aaa_originals/AAAGS_EAGLE2_HRC_r11_2016/aaags.hrc_r11_2016.chr" | ||
|
|
||
| # ### CTMMGS, 1000G phase 3, GoNL5 | ||
| ### CTMMGS, 1000G phase 3, GoNL5 | ||
| # IMPUTEDDATA="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/ctmm_1kGp3GoNL5_RAW_chr" | ||
| ### CTMMGS, 1000G phase 3 (Michigan Imputation Server) | ||
| # IMPUTEDDATA="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_EAGLE2_1000Gp3/ctmmgs.1kgp3.chr" | ||
| ### CTMMGS, HRC r1.1 (Michigan Imputation Server) | ||
| # IMPUTEDDATA="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_EAGLE2_HRC_r11_2016/ctmmgs.hrc_r11_2016.chr" | ||
|
|
||
| # REQUIRED: location of sample file. | ||
| ### REQUIRED: location of sample file. | ||
| # | ||
| # ### AEGS | ||
| ### AEGS | ||
| SAMPLE_FILE="/hpc/dhl_ec/svanderlaan/projects/SOMEDIR/SNP/20201105.LOOKUP.AEGS123.sample" | ||
| SAMPLE_FILE_CHRX="/hpc/dhl_ec/svanderlaan/projects/SOMEDIR/SNP/20201105.LOOKUP.AEGS123.chrX.sample" | ||
|
|
||
| # ### AAAGS | ||
| ### AAAGS | ||
| # SAMPLE_FILE="/hpc/dhl_ec/data/_aaa_originals/pheno_cov_exclusions/aaags_phenocov.sample" | ||
|
|
||
| # ### CTMMGS | ||
| ### CTMMGS | ||
| # SAMPLE_FILE="/hpc/dhl_ec/data/_ctmm_originals/pheno_cov_exclusions/ctmm_phenocov.sample" | ||
|
|
||
| ### REQUIRED: exclusion criteria according to the format "-[in/ex]clude_samples_where <name> [=|==|!=] <value>" | ||
|
|
@@ -141,128 +138,64 @@ SAMPLE_FILE_CHRX="/hpc/dhl_ec/svanderlaan/projects/SOMEDIR/SNP/20201105.LOOKUP.A | |
| ### SampleID123Y | ||
| ### SampleID123Z | ||
|
|
||
| ### DEFAULT | ||
| ### REQUIRED: exclusion requirement; DEFAULT | ||
| EXCLUSION_CRITERIA="-exclude_samples_where \"SELECTION\"==\"not_selected\" " | ||
|
|
||
| # ### AEGS specific exclusion lists | ||
| ### REQUIRED: provide specific exclusion description, no space, all capitals | ||
| EXCLUSION="EXCL_DEFAULT" | ||
| # EXCLUSION_LIST=/hpc/dhl_ec/data/_ae_originals/pheno_cov_exclusions/exclusion_nonCEA.list | ||
| # EXCLUSION="EXCL_FEMALES" | ||
| # EXCLUSION_LIST=/hpc/dhl_ec/data/_ae_originals/pheno_cov_exclusions/exclusion_nonCEA_Females.list | ||
| # EXCLUSION="EXCL_MALES" | ||
| # EXCLUSION_LIST=/hpc/dhl_ec/data/_ae_originals/pheno_cov_exclusions/exclusion_nonCEA_Males.list | ||
| # EXCLUSION="EXCL_CKD" | ||
| # EXCLUSION_LIST=/hpc/dhl_ec/data/_ae_originals/pheno_cov_exclusions/exclusion_nonCEA_CKD.list | ||
| # EXCLUSION="EXCL_NONCKD" | ||
| # EXCLUSION_LIST=/hpc/dhl_ec/data/_ae_originals/pheno_cov_exclusions/exclusion_nonCEA_nonCKD.list | ||
| # EXCLUSION="EXCL_T2D" | ||
| # EXCLUSION_LIST=/hpc/dhl_ec/data/_ae_originals/pheno_cov_exclusions/exclusion_nonCEA_T2D.list | ||
| # EXCLUSION="EXCL_NONT2D" | ||
| # EXCLUSION_LIST=/hpc/dhl_ec/data/_ae_originals/pheno_cov_exclusions/exclusion_nonCEA_nonT2D.list | ||
| # EXCLUSION="EXCL_SMOKER" | ||
| # EXCLUSION_LIST=/hpc/dhl_ec/data/_ae_originals/pheno_cov_exclusions/exclusion_nonCEA_SMOKER.list | ||
| # EXCLUSION="EXCL_NONSMOKER" | ||
| # EXCLUSION_LIST=/hpc/dhl_ec/data/_ae_originals/pheno_cov_exclusions/exclusion_nonCEA_nonSMOKER.list | ||
| # EXCLUSION="EXCL_PRE2007" | ||
| # EXCLUSION_LIST=/hpc/dhl_ec/data/_ae_originals/pheno_cov_exclusions/exclusion_nonCEA_pre2007.list | ||
| # EXCLUSION="EXCL_POST2007" | ||
| # EXCLUSION_LIST=/hpc/dhl_ec/data/_ae_originals/pheno_cov_exclusions/exclusion_nonCEA_post2007.list | ||
| # EXCLUSION="EXCL_DIURETICS" | ||
| # EXCLUSION_LIST=/hpc/dhl_ec/data/_ae_originals/pheno_cov_exclusions/exclusion_nonCEA_DIURETICS.list | ||
| # EXCLUSION="EXCL_NONDIURETICS" | ||
| # EXCLUSION_LIST=/hpc/dhl_ec/data/_ae_originals/pheno_cov_exclusions/exclusion_nonCEA_nonDIURETICS.list | ||
|
|
||
| # ### AAAGS specific exclusion lists | ||
| # EXCLUSION="EXCL_DEFAULT" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_aaa_originals/pheno_cov_exclusions/exclusion_nonAAAGS.list" | ||
| # EXCLUSION="EXCL_FEMALES" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_aaa_originals/pheno_cov_exclusions/exclusion_nonAAAGS_Females.list" | ||
| # EXCLUSION="EXCL_MALES" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_aaa_originals/pheno_cov_exclusions/exclusion_nonAAAGS_Males.list" | ||
| # EXCLUSION="EXCL_CKD" -- does not exist yet | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_aaa_originals/pheno_cov_exclusions/exclusion_nonAAAGS_CKD.list" | ||
| # EXCLUSION="EXCL_NONCKD" -- does not exist yet | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_aaa_originals/pheno_cov_exclusions/exclusion_nonAAAGS_nonCKD.list" | ||
| # EXCLUSION="EXCL_T2D" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_aaa_originals/pheno_cov_exclusions/exclusion_nonAAAGS_T2D.list" | ||
| # EXCLUSION="EXCL_NONT2D" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_aaa_originals/pheno_cov_exclusions/exclusion_nonAAAGS_nonT2D.list" | ||
| # EXCLUSION="EXCL_SMOKER" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_aaa_originals/pheno_cov_exclusions/exclusion_nonAAAGS_SMOKER.list" | ||
| # EXCLUSION="EXCL_NONSMOKER" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_aaa_originals/pheno_cov_exclusions/exclusion_nonAAAGS_nonSMOKER.list" | ||
| # EXCLUSION="EXCL_DIURETICS" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_aaa_originals/pheno_cov_exclusions/exclusion_nonAAAGS_DIURETICS.list" | ||
| # EXCLUSION="EXCL_NONDIURETICS" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_aaa_originals/pheno_cov_exclusions/exclusion_nonAAAGS_nonDIURETICS.list" | ||
| # EXCLUSION="EXCL_DEFAULT_NONAAA" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_aaa_originals/pheno_cov_exclusions/exclusion_nonAAAGSnonAAA.list" | ||
|
|
||
| ### CTMMGS specific exclusion lists | ||
| # EXCLUSION="EXCL_DEFAULT" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/pheno_cov_exclusions/exclusion_nonCTMM.list" | ||
| # EXCLUSION="EXCL_FEMALES" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/pheno_cov_exclusions/exclusion_nonCTMM_FEMALES.list" | ||
| # EXCLUSION="EXCL_MALES" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/pheno_cov_exclusions/exclusion_nonCTMM_MALES.list" | ||
| # EXCLUSION="EXCL_CKD" -- does not exist yet | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/pheno_cov_exclusions/exclusion_nonCTMM_CKD.list" | ||
| # EXCLUSION="EXCL_NONCKD" -- does not exist yet | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/pheno_cov_exclusions/exclusion_nonCTMM_nonCKD.list" | ||
| # EXCLUSION="EXCL_T2D" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/pheno_cov_exclusions/exclusion_nonCTMM_T2D.list" | ||
| # EXCLUSION="EXCL_NONT2D" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/pheno_cov_exclusions/exclusion_nonCTMM_nonT2D.list" | ||
| # EXCLUSION="EXCL_SMOKER" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/pheno_cov_exclusions/exclusion_nonCTMM_SMOKER.list" | ||
| # EXCLUSION="EXCL_NONSMOKER" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/pheno_cov_exclusions/exclusion_nonCTMM_nonSMOKER.list" | ||
| # EXCLUSION="EXCL_DIURETICS" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/pheno_cov_exclusions/exclusion_nonCTMM_DIURETICS.list" | ||
| # EXCLUSION="EXCL_NONDIURETICS" | ||
| # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/pheno_cov_exclusions/exclusion_nonCTMM_nonDIURETICS.list" | ||
|
|
||
| # REQUIRED: ANALYSIS SPECIFIC ARGUMENTS | ||
| # For per-variant analysis | ||
| # EXAMPLE FORMAT | ||
| # rs1234 1 12345567 | ||
| # rs5678 2 12345567 | ||
| # rs4321 14 12345567 | ||
| # rs9876 20 12345567 | ||
| ### REQUIRED: ANALYSIS SPECIFIC ARGUMENTS | ||
| ### For per-variant analysis | ||
| ### EXAMPLE FORMAT | ||
| ### rs1234 1 12345567 | ||
| ### rs5678 2 12345567 | ||
| ### rs4321 14 12345567 | ||
| ### rs9876 20 12345567 | ||
| VARIANTLIST="${PROJECTDIR}/variantlist.txt" | ||
|
|
||
| # REQUIRED: For GWAS, GENE, REGIONAL, and VARIANT analyses -- options: [STANDARDIZE/RAW] | ||
| ### REQUIRED: For GWAS, GENE, REGIONAL, and VARIANT analyses -- options: [STANDARDIZE/RAW] | ||
| STANDARDIZE="RAW" | ||
| # REQUIRED: You can choose one of these method options [expected/score/newml] -- expected is likely best; | ||
| # refer to SNPTEST documentation and more method options. | ||
| # If you choose `-method newml`, you must supply the baseline-phenotype to which the other | ||
| # discrete phenotypes are compared. | ||
| ### REQUIRED: You can choose one of these method options [expected/score/newml] -- expected is likely best; | ||
| ### refer to SNPTEST documentation and more method options. | ||
| ### If you choose `-method newml`, you must supply the baseline-phenotype to which the other | ||
| ### discrete phenotypes are compared. | ||
| METHOD="expected" | ||
| BASELINEPHENOTYPE="control" | ||
| # REQUIRED: You can indicate to condition on a (list of) variant(s) [NORMAL/CONDITION]; refer to SNPTEST documentation. | ||
| ### REQUIRED: You can indicate to condition on a (list of) variant(s) [NORMAL/CONDITION]; refer to SNPTEST documentation. | ||
| CONDITION="NORMAL" | ||
| # CONDITIONLIST="${PROJECTDIR}/conditionvariants.rs2521501.txt" | ||
| CONDITIONLIST="${PROJECTDIR}/conditionvariants.rs17514846.txt" | ||
|
|
||
| # REQUIRED: For GWAS -- make PLINK/this work with VCF files NEW VERSION | ||
| ### REQUIRED: For GWAS -- make PLINK/this work with VCF files NEW VERSION | ||
| CLUMP_P2="1" | ||
| CLUMP_P1="0.000005" # should be of the form 0.005 rather than 5e-3 | ||
| CLUMP_R2="0.2" | ||
| CLUMP_KB="500" | ||
| CLUMP_FIELD="P" | ||
|
|
||
| # REQUIRED: For regional analysis -- handle this via a file! NEW VERSION | ||
| ### REQUIRED: For regional analysis -- handle this via a file! NEW VERSION | ||
| CHR="1" # e.g. 1 | ||
| REGION_START="154376264" # e.g. 154376264 | ||
| REGION_END="154476264" # e.g. 154476264 | ||
|
|
||
| # REQUIRED: For per-gene analysis | ||
| ### REQUIRED: For per-gene analysis | ||
| GENES_FILE="${PROJECTDIR}/genelist.txt" | ||
|
|
||
| # REQUIRED: For GWAS/REGION/GENE analysis | ||
| ### REQUIRED: For GWAS/REGION/GENE analysis | ||
| RANGE="500000" # 500000=500kb, needed for GWAS (LocusZoom plots); and GENE analyses (analysis and LocusZoom plots) | ||
|
|
||
| # REQUIRED: Filter settings -- specifically, GWAS, GENE and REGIONAL analyses | ||
| ### REQUIRED: Filter settings -- specifically, GWAS, GENE and REGIONAL analyses | ||
| INFO="0.3" | ||
| MAC="6" | ||
| CAF="0.005" | ||
|
|
@@ -274,12 +207,12 @@ VARIANTID="2" # this can handle by parseTable! NEW VERSION | |
| PVALUE="17" # this can handle by parseTable! NEW VERSION | ||
| RANGELZ=$(expr "$RANGE" / 1000) # move this to the locuszoom-script! NEW VERSION | ||
|
|
||
| # REQUIRED: References -- these will be created upon installation | ||
| # You can choose one of these options [1kGp3v5GoNL5/1kGp1v3/GoNL4]. | ||
| ### REQUIRED: References -- these will be created upon installation | ||
| ### You can choose one of these options [1kGp3v5GoNL5/1kGp1v3/GoNL4]. | ||
| REFERENCE="1kGp3v5GoNL5" | ||
| REFERENCEDATA="${GWASTOOLKITDIR}/RESOURCES/1000Gp3v5_EUR/1000Gp3v5.20130502.EUR" | ||
| # You can choose one of these: | ||
| # - refSeq based: refseq_GRCh37_hg19_Feb2009.txt.gz | ||
| # - GENCODE based: gencode_v19_GRCh37_hg19_Feb2009.txt.gz | ||
| # - PLINK-style gene list: glist-hg19.gz | ||
| ### You can choose one of these: | ||
| ### - refSeq based: refseq_GRCh37_hg19_Feb2009.txt.gz | ||
| ### - GENCODE based: gencode_v19_GRCh37_hg19_Feb2009.txt.gz | ||
| ### - PLINK-style gene list: glist-hg19.gz | ||
| HG19_GENES="${GWASTOOLKITDIR}/RESOURCES/glist-hg19.gz" | ||